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<thread>

  <info>
    
    <version>June 2009</version>
    <title>
      <long>Contours</long>
    </title>
    <history>
      <entry day="24" month="June" year="9" who="liz">
	Original version
	<!-- copied in part from CIAO ds9 thread //-->
     </entry>
     </history>
  </info>

  <text>
    <overview>

      <synopsis>
        <p>
	  Contours are shapes which are drawn on the data at a
	  specified pixel value.  ds9 can create and display contours
	  as an overlay on an image.  
	</p>
      </synopsis>
    </overview>

    <sectionlist>

      <section id="create">
        <title>Creating Contours on a Dataset</title>

	<p>
	  This thread uses Chandra data from an observation of the
	  galaxy cluster Abell 2142 (ObsID 5005).
	</p>

        <p>
	  After loading the data into ds9 and setting the desired
	  scale, click on the "Contours" item in the "Analysis" menu
	  to turn on contour display.  Open the "Contour Parameters"
	  window from "Analysis &#8594; Contours Parameters".  There
	  are two sliding scales which are used to set the number and
	  smoothness of the contours and fields for setting the range
	  of values to use. 
	</p>

	<figure id="dialog">
	  <title>Contour Parameters dialog box</title>
	  <description>The "Contour Parameters" dialog box has sliding
	  scales to set the number and smoothness of the contours and
	  fields for setting the range of values.</description>  
	  <bitmap format="png">dialog.png</bitmap>
	</figure> 

	<p>
	  Typically, you will want to generate between 1 and 10
	  contours; larger numbers will take longer to generate and
	  display.  A smoothness level of 1 will evaluate the contour
	  at each image pixel, while a level of 2 will evaluate the
	  contour at every other pixel, and so on.  A larger smoothing
	  will generate contours more quickly, but less detail will be
	  available. 
	</p>
	 
	<p>
	  By default, the range of the data scale is filled in as the
	  limits.  Under the "Method" menu, there are two choices:
	</p>

	<list type="1">
	  <li>
	    block (the default) - blocks down the image by the
	    smoothness factor before contours are calculated.  The
	    larger the smoothness, the faster the result.  
	  </li>

	  <li>
	    smooth - smooths the image before calculating contours.
	    The larger the smoothness, the slower the result. 
	  </li>
	</list>	

	<p>
	  In this example, the number of levels is set to 6 and the
	  smoothing is set to 5.  The contours will be generated over
	  the limit 1 to 100.  The default method (block) is used.
	</p>

	<p>
	  After clicking the "Generate" button, the list of contours
	  is calculated and displayed in the "Levels" portion of the window.
	   Click "Apply" and the ds9 display is updated with the new
	   contour levels, as shown in <figlink id="xraycontour"/>.
	 </p>

	 <figure id="xraycontour">
	   <title>X-ray data with contours</title>
	   <description>Diffuse emission with
	   contours overlaid; a point source is visible in the upper
	   left corner of the image.</description>  
	   <bitmap format="png">xraycontour.png</bitmap>
	 </figure> 

	 <p>
	   The contour parameters can be adjusted until the desired
	   result is achieved.  Be sure to click "Generate" whenever
	   an adjustment is made so that the levels are recalculated.
	 </p>

      </section>

      <section id="copy">
        <title>Copying the Contours to Another Frame</title>

	<p>
	  In this section, we take the X-ray contours just generated
	  and display them on an optional image from the Digital Sky Survey (DSS).
	</p>
	 
	<p>
	  From the "Analysis &#8594; Image Servers" menu, select one
	  of the DSS server options (e.g. "SAO-DSS").  The server
	  dialog box allows you to retrieve an optical image of the
	  field of your observation and load it into a new frame.  The
	  default retrieval image size and (RA,Dec) is equal to the
	  size and center of the field currently displayed.  Here the
	  width and height have been set to 40, but the (RA,Dec)
	  determined by ds9 are used.
	</p>

	<figure id="dssdialog">
	  <title>SAO-DSS Server dialog box</title>
	  <description>The fields for Ra, Dec, width, and height are
	  populated with values determined from the x-ray data image.</description>  
	  <bitmap format="png">dssdialog.png</bitmap>
	</figure> 

	<p>
	  Click on "Retrieve" and the data is loaded into a new ds9
	  frame.  
	</p>

	<p>
	  To copy the x-ray contours:
	</p>

	<list type="1">
	  <li><p>
	    Select the frame with the X-ray data in it.
	  </p></li>
	  <li><p>
	    Use "Frame &#8594; Match Frames &#8594; WCS" to align the
	    two images.
	  </p></li>	
	  <li><p>
	    To copy the contours, open the "Contour Parameters"
	    dialog again and select "Copy Contours" from the
	    "File" menu. Leave the window open, as it is needed in
	    a future step. 
          </p></li>
	  <li><p>
	    Select the frame with the optical data in it.
	  </p></li>
	  <li><p>
	    Using the "File" menu of the "Contour Parameters"
	    dialog, select "Paste Contours".
	  </p></li>
	  <li><p>
	    Adjust the parameters (if desired) in the small dialog box
	    that is displayed, then click "OK".
	  </p></li>
	</list>

	<p>
	  The optical image now has the x-ray contours overlaid.
	  Since the WCS is the same, correlation between x-ray
	  and optical features may be seen.
	</p>

        <figure id="dsscontour">
	  <title>X-ray and optical data with contours</title>
	  <description>The x-ray data is in the left frame and the
	    optical data is in the right frame; both have the x-ray
	    contours displayed on the data.</description>
	  <bitmap format="png">dsscontour.png</bitmap>
	</figure> 

	<p>
	  To delete contours which have been pasted into a
	  frame, select "Clear" from the "File" menu of the "Contour
	  Parameters" dialog.
	</p>
	
      </section>

      <section id="save">
        <title>Saving the Contours</title>

	<p>
	  To save the contours to a text file, choose "Save Contours"
	  from the "File" menu of the "Contour Parameters" dialog.
	  The contours are saved in a text file which can be loaded
	  back into ds9 with the "Open Contours" menu item. 
	</p>

	<p>
	  The contours generated in this thread have been saved as <a href="ds9.con">ds9.con</a>.
	</p>

      </section>

      <section id="convert">
        <title>Converting to Polygons and Saving</title>

	<p>
	  The contours can be converted to ds9 polygon regions for use
	  in filtering data.  Converting to polygons also allows you
	  to select and/or delete specific contours.
	</p>

	<p>
	  <strong>Note that the contours cannot be <threadlink id="save">saved
	  in ds9 format</threadlink> after converting.</strong>  If you wish to
	  save the contours, do so before continuing.
	</p>

	<p>
	  To convert the contours, select "Convert to Polygons" from
	  the "File" menu of the "Contour Parameters" dialog.  The
	  contours are now defined as ds9 polygons, e.g.  
	</p>

<screen>
polygon(3535.2112,4184.5,3540.5,4179.1154,3548.5,4176.8219,3555.9012,4184.5,3548.5,4191.9558,3540.5,4190.3926)
</screen>


	<p>
	  The polygon-shaped contours can be saved as a ds9 region
	  file from the "Region Save &#8594; Regions" menu. The region
	  file for these contours has been saved as <a href="a2142.reg">a2142.reg</a>. 
	</p>
	
      </section>


    </sectionlist>
  </text>

</thread>



